Turkey Egg-white Lysozyme Research Articles

A dipicolinate lanthanide complex for solving protein structures using anomalous diffraction

Tris-dipicolinate lanthanide complexes were used to prepare derivative crystals of six proteins: hen egg-white lysozyme, turkey egg-white lysozyme, thaumatin from Thaumatococcus daniellii, urate oxidase from Aspergillus flavus, porcine pancreatic elastase and xylanase from Trichoderma reesei. Diffraction data were collected using either synchrotron radiation or X-rays from a laboratory source. In all cases, the complex turned out to be bound to the protein and the phases determined using the anomalous scattering of the lanthanide led to high-quality electron-density maps. The binding mode of the complex was characterized from the refined structures. The lanthanide tris-dipicolinate was found to bind through interactions between carboxylate groups of the dipicolinate ligands and hydrogen-bond donor groups of the protein. In each binding site, one enantiomeric form of the complex is selected from the racemic solution according to the specific site topology. For hen egg-white lysozyme and xylanase, derivative crystals obtained by cocrystallization belonged to a new monoclinic C2 crystal form that diffracted to high resolution.

The distribution of impurities in lysozyme crystals

The effective distribution coefficient, K Ieff , of turkey egg white lysozyme into host hen egg white lysozyme crystals was measured for varying levels of relative supersaturation, impurity concentrations and temperatures. Turkey egg white lysozyme served as a test impurity of high homology to hen egg white lysozyme. K Ieff increased with increasing host protein concentration and temperature, consistent with a kinetically controlled incorporation process. The principles of slow crystal growth rate to limit impurity incorporation were applied to a commercial source of lysozyme with concomitant improvement in purity of re-crystallized protein.

Protein–protein recognition and interaction hot spots in an antigen–antibody complex: Free energy decomposition identifies “efficient amino acids”

The molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) method was applied to the study of the protein-protein complex between a camelid single chain variable domain (cAb-Lys3) and hen egg white lysozyme (HEL), and between cAb-Lys3 and turkey egg white lysozyme (TEL). The electrostatic energy was estimated by solving the linear Poisson-Boltzmann equation. A free energy decomposition scheme was developed to determine binding energy hot spots of each complex. The calculations identified amino acids of the antibody that make important contributions to the interaction with lysozyme. They further showed the influence of small structural variations on the energetics of binding and they showed that the antibody amino acids that make up the hot spots are organized in such a way as to mimic the lysozyme substrate. Through further analysis of the results, we define the concept of "efficient amino acids," which can provide an assessment of the binding potential of a particular hot spot interaction. This information, in turn, can be useful in the rational design of small molecules that mimic the antibody. The implications of using free energy decomposition to identify regions of a protein-protein complex that could be targeted by small molecules inhibitors are discussed.

Crystal quality and differential crystal-growth behaviour of three proteins crystallized in gel at high hydrostatic pressure

Pressure is a non-invasive physical parameter that can be used to control and influence protein crystallization. It is also found that protein crystals of superior quality can be produced in gel. Here, a novel crystallization strategy combining hydrostatic pressure and agarose gel is described. Comparative experiments were conducted on hen and turkey egg-white lysozymes and the plant protein thaumatin. Crystals could be produced under up to 75-100 MPa (lysozymes) and 250 MPa (thaumatin). Several pressure-dependent parameters were determined, which included solubility and supersaturation of the proteins, number, size and morphology of the crystals, and the crystallization volume. Exploration of three-dimensional phase diagrams in which pH and pressure varied identified growth conditions where crystals had largest size and best morphology. As a general trend, nucleation and crystal-growth kinetics are altered and nucleation is always enhanced under pressure. Further, solubility of the lysozymes increases with pressure while that of thaumatin decreases. Likewise, changes in crystallization volumes at high and atmospheric pressure are opposite, being positive for the lysozymes and negative for thaumatin. Crystal quality was estimated by analysis of Bragg reflection profiles and X-ray topographs. While the quality of lysozyme crystals deteriorates as pressure increases, that of thaumatin crystals improves, with more homogeneous crystal morphology suggesting that pressure selectively dissociates ill-formed nuclei. Analysis of the thaumatin structure reveals a less hydrated solvent shell around the protein when pressure increases, with approximately 20% less ordered water molecules in crystals grown at 150 MPa when compared with those grown at atmospheric pressure (0.1 MPa). Noticeably, the altered water distribution is seen in depressurized crystals, indicating that pressure triggers a stable structural alteration on the protein surface while its polypeptide backbone remains essentially unaltered.

Synchrotron X-ray powder diffraction study of hexagonal turkey egg-white lysozyme

The structure of turkey egg-white lysozyme (TEWL) has been refined from high-resolution X-ray powder diffraction data. The sample was rapidly obtained as a polycrystalline precipitate at high protein concentration using 0.5 M NaCl solvent pH 6 and was deposited in the PDB with code 1xft. The diffraction data were collected at room temperature. Molecular replacement was shown to give a suitable starting point for refinement, illustrating that powder data can be sufficient for this approach. Crystallographic models were then refined by combined Rietveld and stereochemical restraint analysis of the powder data (d(min) = 3.35 A), resulting in the extraction of reliable lattice parameters and the refinement of the molecular conformation at room temperature. The structure is hexagonal [space group P6(1)22, unit-cell parameters a = 71.0862 (3), c = 85.0276 (5) A] with 12 symmetry-related molecules in the unit cell, in agreement with previous studies. The results of our analysis are indicative of specific amino acids being disordered at this temperature. Upon cooling, a sudden drop in the lattice parameters at approximately 250 K is observed concurrently with the freezing of the mother liquor. The observation of severe peak broadening below this temperature indicates strain effects accompanying the freezing transition, which are found to be reversible. Finally, a correlation between the unit-cell parameters and the pH of the buffer solution is evident, in a similar manner to earlier observations on HEWL.

Re-evaluation of intramolecular long-range electron transfer between tyrosine and tryptophan in lysozymes. Evidence for the participation of other residues.

One-electron oxidation of six different c-type lysozymes from hen egg white, turkey egg white, human milk, horse milk, camel stomach and tortoise was studied by gamma- and pulse-radiolysis. In the first step, one tryptophan side chain is oxidized to indolyl free radical, which is produced quantitatively. As shown already, the indolyl radical subsequently oxidizes a tyrosine side chain to the phenoxy radical in an intramolecular reaction. However this reaction is not total and its stoichiometry depends on the protein. Rate constants also vary between proteins, from 120 x s(-1) to 1000 x s(-1) at pH 7.0 and room temperature [extremes are hen and turkey egg white (120 x s(-1)) and human milk (1000 x s(-1))]. In hen and turkey egg white lysozymes we show that another reactive site is the Asn103-Gly104 peptidic bond, which gets broken radiolytically. Tryptic digestion followed by HPLC separation and identification of the peptides was performed for nonirradiated and irradiated hen lysozyme. Fluorescence spectra of the peptides indicate that Trp108 and/or 111 remain oxidized and that Tyr20 and 53 give bityrosine. Tyr23 appears not to be involved in the process. Thus new features of long-range intramolecular electron transfer in proteins appear: it is only partial and other groups are involved which are silent in pulse radiolysis.

Structural energetics of protein-carbohydrate interactions: Insights derived from the study of lysozyme binding to its natural saccharide inhibitors.

High-sensitivity isothermal titration calorimetry was used to characterize the binding of the glycohydrolitic enzyme hen egg-white lysozyme to its natural saccharide inhibitors, chitobiose and chitrotriose. Measurements were done at a pH of 4.7, in the 15 degrees C -45 degrees C temperature range. Using a structural-energetic parameterization derived previously for lectin-carbohydrate associations, both binding enthalpies and entropies for the present systems and for the complex of chitobiose with turkey egg-white lysozyme from the literature were correctly accounted for. These observations suggest that both lysozymes and lectins follow the same structural-energetic behavior in the binding to their ligands. From the analysis of lysozyme data in conjunction with other binding data reported in the literature, an ad hoc parameterization of DeltaCp for protein-carbohydrate complexes was derived for the first time. The novel parameters for both polar and apolar surface areas differed significantly from correlations obtained previously from model compounds and protein-folding data. As DeltaCp is extremely sensitive to changes in solvent structure, this finding indicates that protein-carbohydrate complexes have distinctive hydration properties. According to our analysis, the dehydration of polar groups is the major cause for the observed decrease in DeltaCp, which implies that these groups behave hydrophobically. The contribution of apolar surface areas was found of the expected sign, but their specific weight is much smaller than those obtained in other correlations. This small contribution to DeltaCp is consistent with Lemieux's hypothesis of a low degree of hydration of apolar surfaces on carbohydrates.

Influence of impurities on protein crystal perfection

A quasi-planar X-ray study has been done to assess the quality of crystals of pure thaumatin and of hen egg-white lysozyme as well as of lysozyme which was intentionally contaminated by structurally unrelated (ovalbumin and conalbumin) or related (turkey egg-white lysozyme) macromolecules. To investigate the behavior of different growth sectors, we have chosen crystals exhibiting well defined habit, namely crystals grown either in agarose gel or in silica gel. The main defect evidenced is a misorientation originating at the level of the nucleus: the parts grown in the + c and − c directions seem to be individuals twisted always clockwise with respect to the growth direction. The measured lattice plane tilt increases up to 3.5 min of arc when the contaminant content increases. In addition to this defect, we could measure for lysozyme relative lattice parameters differences (Δ d/ d) of the order of 10 −4 between prismatic and pyramidal growth sectors. All these defects do not seem to have a major influence on the resolution limit but they have consequences on optical properties.

Affinity chromatography of proteins on non-porous copolymerized particles of styrene, methyl methacrylate and glycidyl methacrylate

Non-porous particles having an average diameter of 2.1 μm were prepared by co-polymerization of styrene, methyl methacrylate and glycidyl methacrylate, which was abbreviated as P(S–MMA–GMA). The particles were mechanically stable due to the presence of benzene rings in the backbone of polymer chains, and could withstand high pressures when a column packed with these particles was operated in the HPLC mode. The polymer particles were advantaged by immobilization of ligands via the epoxy groups on the particle surface that were introduced by one of the monomers, glycidyl methacrylate. As a model system, Cibacron Blue 3G-A was covalently immobilized onto the non-porous copolymer beads. The dye-immobilized P(S–MMA–GMA) particles were slurry packed into a 1.0 cm×0.46 cm I.D. column. This affinity column was effective for the separation of turkey egg white lysozyme from a protein mixture. The bound lysozyme could be eluted to yield a sharp peak by using a phosphate buffer containing 1 M NaCl. For a sample containing up to 8 μg of lysozyme, the retained portion of proteins could be completely eluted without any slit peak. Due to the use of a shorter column, the analysis time was shorter in comparison with other affinity systems reported in the literature. The retention time could be reduced significantly by increasing the flow-rate, while the capacity factor remained at the same level.

Crystal structure of a phage library-derived single-chain fv fragment complexed with turkey egg-white lysozyme at 2.0 Å resolution

The three-dimensional structure of the single-chain Fv fragment 1F9 in complex with turkey egg-white lysozyme (TEL) has been determined to a nominal resolution of 2.0 Å by X-ray diffraction. The scFv fragment 1F9 was derived from phage-display libraries in two steps and binds both hen and turkey egg-white lysozyme, although the level of binding affinity is two orders of magnitude greater for the turkey lysozyme. The comparison of the crystal structure with a model of the single-chain Fv fragment 1F9 in complex with hen egg-white lysozyme (HEL) reveals that in the latter a clash between Asp101 in lysozyme and Trp98 of the complementarity determining region H3 of the heavy chain variable domain occurs. This is the only explanation apparent from the crystal structure for the better binding of TEL compared to HEL.The binding site topology on the paratope is not simply a planar surface as is usually found in antibody-protein interfaces, but includes a cleft between the light chain variable domain and heavy chain variable domain large enough to accommodate a loop from the lysozyme. The scFv fragment 1F9 recognizes an epitope on TEL that differs from the three antigenic determinants recognized in other known crystal structures of monoclonal antibodies in complex with lysozyme.

Oxidative Dimerization of Proteins: Role of Tyrosine Accessibility

Purpose. To investigate the importance of two possible mechanisms of tyrosine oxidation on the yield of protein dimerization. The model chosen is hen and turkey egg-white lysozymes, which differ by seven amino acids, among which one tyrosine is in the 3 position. Materials and methods. Aqueous solutions of proteins were oxidized by OH• or N•3 free radicals produced by γ or pulse irradiation in an atmosphere of N2O. Protein dimers were quantified by SDS–PAGE and reverse-phase HPLC. Dityrosines were identified by absorption and fluorescence. Results. Using N•3 free radicals, the initial yields of dimerization are equal to (8.6 ± 0.7) × 10−9 mol J−1 for both proteins. Using OH• free radicals, they become equal to (1.23 ± 0.1) × 10−8 and (4.42 ± 0.1) × 10−8 mol J−1 for hen and turkey egg-white lysozymes, respectively (γ radiolysis). Discussion. N•3 radicals react primarily with tryptophan residues only. Tyrosine gets oxidized by intramolecular long-range electron migration, whereas OH• may react directly with tyrosines. We propose a low participation of Tyr3 in turkey protein in the intramolecular process, because Tyr3 is far from all tryptophans. On the other hand, Tyr3 is very accessible to solvent and in a flexible area; thus collisions with OH• could easily be followed by intermolecular dimerization.

Macromolecular impurities and disorder in protein crystals

The mechanisms by which macromolecular impurities degrade the diffraction properties of protein crystals have been investigated using X-ray topography, high-resolution diffraction line shape measurements, crystallographic data collection, chemical analysis, and two-photon excitation fluorescence microscopy. Hen egg-white lysozyme crystals grown from solutions containing a structurally unrelated protein (ovotransferrin) and a related protein (turkey egg-white lysozyme) can exhibit significantly broadened mosaicity due to formation of cracks and dislocations but have overall B factors and diffraction resolutions comparable to those of crystals grown from uncontaminated lysozyme. Direct fluorescence imaging of the three-dimensional impurity distribution shows that impurities incorporate with different densities in sectors formed by growth on different crystal faces, and that impurity densities in the crystal core and along boundaries between growth sectors can be much larger than in other parts of the crystal. These nonuniformities create stresses that drive formation of the defects responsible for the mosaic broadening. Our results provide a rationale for the use of seeding to obtain high-quality crystals from heavily contaminated solutions and have implications for the use of crystallization for protein purification. Proteins 1999;36:270-281.

Macromolecular impurities and disorder in protein crystals

The mechanisms by which macromolecular impurities degrade the diffraction properties of protein crystals have been investigated using X-ray topography, high-resolution diffraction line shape measurements, crystallographic data collection, chemical analysis, and two-photon excitation fluorescence microscopy. Hen egg-white lysozyme crystals grown from solutions containing a structurally unrelated protein (ovotransferrin) and a related protein (turkey egg-white lysozyme) can exhibit significantly broadened mosaicity due to formation of cracks and dislocations but have overall B factors and diffraction resolutions comparable to those of crystals grown from uncontaminated lysozyme. Direct fluorescence imaging of the three-dimensional impurity distribution shows that impurities incorporate with different densities in sectors formed by growth on different crystal faces, and that impurity densities in the crystal core and along boundaries between growth sectors can be much larger than in other parts of the crystal. These nonuniformities create stresses that drive formation of the defects responsible for the mosaic broadening. Our results provide a rationale for the use of seeding to obtain high-quality crystals from heavily contaminated solutions and have implications for the use of crystallization for protein purification. Proteins 1999;36:270–281. © 1999 Wiley-Liss, Inc.

Characterization of protein and virus crystals by quasi-planar wave X-ray topography: a comparison between crystals grown in solution and in agarose gel

Quasi-planar wave reflection profile and X-ray topography studies have been done to characterize the mosaicity of solution- and gel-grown crystals of three proteins, turkey egg-white (TEW) lysozyme, thaumatin, and a bacterial aspartyl-tRNA synthetase (AspRS) as well as of one virus, tomato bushy stunt virus (TBSV). These materials are representative of a large range of molecular weight, overall particle shapes, crystals habits, packings, and solvent contents. Measurements of the full-width at half-maximum (FWHM) of reflections show that these different crystals have all a weak mosaicity. Topographs display the same features as those of the well-studied hen egg-white (HEW) lysozyme crystals: misorientation generated at the seed level for TEW lysozyme or thaumatin crystals and/or strains at growth sector boundaries for AspRS crystals. No growth defects are evidenced for TBSV crystals. For the study of crystals diffracting at lower resolution (AspRS and virus), a less absorbant sample holder, which facilitates crystal positioning in the X-ray beam, has been developed. The results obtained for solution- and gel-grown crystals do not show important differences. However, for TEW lysozyme and thaumatin crystals, one notices a larger dispersion of results in the solution case and an overall tendency for improved reproducibility of quality for gel-grown crystals.

Additives for the crystallization of proteins and nucleic acids

Numerous molecules have been described in literature as additives that were indispensable either for nucleation or growth of macromolecular crystals. In some cases, such additives were shown to improve the quality of the X-ray diffraction and to extend diffraction limits. We have investigated the effects of more than fifty compounds, belonging to several chemical families, on the crystallization of four model proteins (hen and turkey egg-white lysozymes, thaumatin, and aspartyl-tRNA synthetase from Thermus thermophilus). In addition, we have studied the crystallization of a ribonucleic acid from yeast, the transfer RNA specific for phenylalanine in the presence of synthetic polyamines. Crystals grown in the presence of the additives were optically evaluated and X-ray diffraction analyses were performed on selective crystals to compare their space group, cell parameters, and diffraction limit with those of controls. Whereas no changes in space group nor cell parameters were observed for the model proteins, significant improvements in diffraction limit were found when the transfer RNA was crystallized with certain synthetic polyamines.

A phage library-derived single-chain Fv fragment in complex with turkey egg-white lysozyme: characterization, crystallization and preliminary X-ray analysis

Using phage-display, an anti-turkey egg-white lysozyme single-chain Fv fragment was selected from a naive light chain variable region repertoire in combination with a heavy chain variable region ‘mini library‘ of anti-hen egg-white lysozyme single-domain binders ( Ward et al., 1989). Whereas the selected V H domain alone binds somewhat better hen egg-white lysozyme than turkey egg-white lysozyme, but both with comparatively low affinity, the specificity of V H is converted by addition of the V L domain. Thus, the single-chain Fv fragment is more specific for turkey egg-white lysozyme, with markedly increased affinities towards both lysozymes. The complex of single-chain Fv with turkey lysozyme has been crystallized and characterized by preliminary X-ray analysis.

Contaminant inclusion into protein crystals analyzed by electrospray mass spectrometry and X-ray crystallography.

The inclusion of protein contaminants into crystals of turkey egg white lysozyme (TEWL) was investigated by electrospray mass spectrometry of the dissolved crystals. The results show that significant amounts of the structurally related contaminant hen egg white lysozyme (HEWL) are included in the crystals of TEWL. The structurally unrelated contaminant RNAse A, on the other hand, is not included. The X-ray diffraction data statistics of a hybrid TEWL/HEWL crystal and an uncontaminated TEWL crystal were of similar quality. This indicates that, even though the crystals contain much higher levels of the contaminant than one would have expected after a recrystallization experiment, they are still suitable for X-ray diffraction experiments. However, attempts to detect the presence of the contaminant in the crystal by crystallographic structure refinement did not yield conclusive results.

Protein crystal growth rates are face-specifically modified by structurally related contaminants

Growth rates of turkey egg-white lysozyme (TEWL) crystal faces have been measured in uncontaminated solutions as well as in solutions contaminated by the homologous hen egg-white lysozyme (HEWL). Comparison of growth rates from uncontaminated and contaminated solutions shows that the growth rate of the {112} faces drops significantly in the presence of the contaminant, whereas the growth rate of the {110} faces does not change. This demonstrates that HEWL acts specifically on the growth process of the {112} faces.

Contaminant effects on protein crystal morphology in different growth environments.

Contaminant effects on the morphology of turkey egg-white lysozyme (TEWL) crystals grown in ungelled and in gelled growth media have been investigated. The latter may serve as a model system for future microgravity experiments. Hen egg-white lysozyme (HEWL) was added as the contaminant at levels ranging from 4 up to 70%(w/w) (total protein). Morphology measurements indicate a contaminant effect leading to a shortening along the c axis of the crystal. This shortening effect depends on the contaminant concentration. It is attenuated and varies more regularly in gelled than in ungelled growth media. The specificity of the HEWL contaminant effect was verified by addition of ribonuclease A, which did not influence crystal morphology. Contaminant inclusion into the growing TEWL crystals could be calculated directly from equilibrium protein concentration measurements. The level of HEWL inclusion is closely related to the concentration of HEWL in the growth solutions. The specificity of the observed effect as well as the differences between the two growth media are discussed.

The effects of filtration on protein nucleation in different growth media.

Filtration effects of turkey egg white lysozyme solution (TEWL) prior to subjecting it to crystallization conditions are investigated. Filtering TEWL solution and crystallizing it in ungelled media significantly decreased the number of conditions yielding crystals. This decrease dependent on the membrane cut-off used for filtration. From this, the postulated factors aiding in nucleation are estimated to be 0.17 microns in diameter. The existence of these factors was verified by the procedure of reversed filtration: filtered solutions passed through their inverted filter membrane a second time lead to improved crystallization results. The effect of aging of the TEWL solution prior to subjecting it to ungelled crystallization conditions was also verified. We did not find any time-dependent change in the size or the number of crystals per drop. Repeating the filtration experiments in agarose-gelled crystallization media showed that the influence of filtration on the crystallization outcome was significantly diminished. Far better crystallization results were obtained compared to ungelled media. However, there is a certain aging effect linked to filtration in gelled media. Different crystallization results were obtained depending on whether filtration was performed before or after aging and subsequent crystallization. This suggests a secondary time-dependent effect.